Login Register Cart 0
Generic placeholder image

Current Medicinal Chemistry

Editor-in-Chief

ISSN (Print): 0929-8673
ISSN (Online): 1875-533X

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe Translate in Chinese
Review Article

Protein Interaction Domains: Structural Features and Drug Discovery Applications (Part 2)

Author(s): Marian Vincenzi, Flavia Anna Mercurio and Marilisa Leone*

Volume 28, Issue 5, 2021

Published on: 14 January, 2020

Page: [854 - 892] Pages: 39

DOI: 10.2174/0929867327666200114114142

Price: $65

Abstract

Background: Proteins present a modular organization made up of several domains. Apart from the domains playing catalytic functions, many others are crucial to recruit interactors. The latter domains can be defined as "PIDs" (Protein Interaction Domains) and are responsible for pivotal outcomes in signal transduction and a certain array of normal physiological and disease-related pathways. Targeting such PIDs with small molecules and peptides able to modulate their interaction networks, may represent a valuable route to discover novel therapeutics.

Objective: This work represents a continuation of a very recent review describing PIDs able to recognize post-translationally modified peptide segments. On the contrary, the second part concerns with PIDs that interact with simple peptide sequences provided with standard amino acids.

Methods: Crucial structural information on different domain subfamilies and their interactomes was gained by a wide search in different online available databases (including the PDB (Protein Data Bank), the Pfam (Protein family), and the SMART (Simple Modular Architecture Research Tool)). Pubmed was also searched to explore the most recent literature related to the topic.

Results and Conclusion: PIDs are multifaceted: they have all diverse structural features and can recognize several consensus sequences. PIDs can be linked to different diseases onset and progression, like cancer or viral infections and find applications in the personalized medicine field. Many efforts have been centered on peptide/peptidomimetic inhibitors of PIDs mediated interactions but much more work needs to be conducted to improve drug-likeness and interaction affinities of identified compounds.

Keywords: Protein interaction domains, protein-protein interactions, structure, drug discovery, ligands, inhibitors, peptides, small molecules.

« Previous Next »
[1]
Mayer, B.J. Protein-protein interactions in signaling cascades. Mol. Biotechnol., 1999, 13(3), 201-213.
[http://dx.doi.org/10.1385/MB:13:3:201] [PMID: 10934533]
[2]
Pawson, T.; Raina, M.; Nash, P. Interaction domains: from simple binding events to complex cellular behavior. FEBS Lett., 2002, 513(1), 2-10.
[http://dx.doi.org/10.1016/S0014-5793(01)03292-6] [PMID: 11911873]
[3]
Pawson, T. Protein modules and signalling networks. Nature, 1995, 373(6515), 573-580.
[http://dx.doi.org/10.1038/373573a0] [PMID: 7531822]
[4]
Pawson, T.; Nash, P. Assembly of cell regulatory systems through protein interaction domains. Science, 2003, 300(5618), 445-452.
[http://dx.doi.org/10.1126/science.1083653] [PMID: 12702867]
[5]
Liu, B.A.; Engelmann, B.W.; Nash, P.D. High-throughput analysis of peptide-binding modules. Proteomics, 2012, 12(10), 1527-1546.
[http://dx.doi.org/10.1002/pmic.201100599] [PMID: 22610655]
[6]
Zarrinpar, A.; Bhattacharyya, R.P.; Lim, W.A. The structure and function of proline recognition domains. Sci. STKE, 2003, 2003(179), RE8.
[http://dx.doi.org/10.1126/stke.2003.179.re8] [PMID: 12709533]
[7]
Polo, S. Confalonieri, S.; Salcini, A.E.; Di Fiore, P.P. EH and UIM: endocytosis and more. Sci. STKE, 2003, 2003(213), re17.
[http://dx.doi.org/10.1126/stke.2132003re17] [PMID: 14679291]
[8]
Montesinos, M.L.; Castellano-Muñoz, M.; García-Junco-Clemente, P.; Fernández-Chacón, R. Recycling and EH domain proteins at the synapse. Brain Res. Brain Res. Rev., 2005, 49(2), 416-428.
[http://dx.doi.org/10.1016/j.brainresrev.2005.06.002] [PMID: 16054223]
[9]
Chi, C.N.; Bach, A.; Strømgaard, K.; Gianni, S.; Jemth, P. Ligand binding by PDZ domains. Biofactors, 2012, 38(5), 338-348.
[http://dx.doi.org/10.1002/biof.1031] [PMID: 22674855]
[10]
Brown, S.; Coghill, I.D.; McGrath, M.J.; Robinson, P.A. Role of LIM domains in mediating signaling protein interactions. IUBMB Life, 2001, 51(6), 359-364.
[http://dx.doi.org/10.1080/152165401753366113] [PMID: 11758803]
[11]
Korenbaum, E.; Rivero, F. Calponin homology domains at a glance. J. Cell Sci., 2002, 115(Pt 18), 3543-3545.
[http://dx.doi.org/10.1242/jcs.00003] [PMID: 12186940]
[12]
Dalgarno, D.C.; Botfield, M.C.; Rickles, R.J. SH3 domains and drug design: ligands, structure, and biological function. Biopolymers, 1997, 43(5), 383-400.
[http://dx.doi.org/10.1002/(SICI)10970282(1997)43:5< 383:AID-BIP4>3.0.CO;2-R] [PMID: 9566119]
[13]
Renfranz, P.J.; Beckerle, M.C. Doing (F/L)PPPPs: EVH1 domains and their proline-rich partners in cell polarity and migration. Curr. Opin. Cell Biol., 2002, 14(1), 88-103.
[http://dx.doi.org/10.1016/S0955-0674(01)00299-X] [PMID: 11792550]
[14]
Peterson, F.C.; Volkman, B.F. Diversity of polyproline recognition by EVH1 domains. Front. Biosci., 2009, 14, 833-846.
[http://dx.doi.org/10.2741/3281] [PMID: 19273103]
[15]
Nishizawa, K.; Freund, C.; Li, J.; Wagner, G.; Reinherz, E.L. Identification of a proline-binding motif regulating CD2-triggered T lymphocyte activation. Proc. Natl. Acad. Sci. USA, 1998, 95(25), 14897-14902.
[http://dx.doi.org/10.1073/pnas.95.25.14897] [PMID: 9843987]
[16]
Hurley, J.H.; Lee, S.; Prag, G. Ubiquitin-binding domains. Biochem. J., 2006, 399(3), 361-372.
[http://dx.doi.org/10.1042/BJ20061138] [PMID: 17034365]
[17]
Sang, M.; Ma, L.; Sang, M.; Zhou, X.; Gao, W.; Geng, C. LIM-domain-only proteins: multifunctional nuclear transcription coregulators that interacts with diverse proteins. Mol. Biol. Rep., 2014, 41(2), 1067-1073.
[http://dx.doi.org/10.1007/s11033-013-2952-1] [PMID: 24379077]
[18]
Bañuelos, S.; Saraste, M.; Djinović Carugo, K. Structural comparisons of calponin homology domains: implications for actin binding. Structure, 1998, 6(11), 1419-1431.
[http://dx.doi.org/10.1016/S0969-2126(98)00141-5] [PMID: 9817844]
[19]
Confalonieri, S.; Di Fiore, P.P. The Eps15 homology (EH) domain. FEBS Lett., 2002, 513(1), 24-29.
[http://dx.doi.org/10.1016/S0014-5793(01)03241-0] [PMID: 11911876]
[20]
Qiao, F.; Bowie, J.U. The many faces of SAM. Sci. STKE, 2005, 2005(286), re7.
[http://dx.doi.org/10.1126/stke.2862005re7 ] [PMID: 15928333]
[21]
Haura, E.B. From modules to medicine: How modular domains and their associated networks can enable personalized medicine? FEBS Lett., 2012, 586(17), 2580-2585.
[http://dx.doi.org/10.1016/j.febslet.2012.04.036] [PMID: 22575759]
[22]
Taylor, I.W.; Linding, R.; Warde-Farley, D.; Liu, Y.; Pesquita, C.; Faria, D.; Bull, S.; Pawson, T.; Morris, Q.; Wrana, J.L. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat. Biotechnol., 2009, 27(2), 199-204.
[http://dx.doi.org/10.1038/nbt.1522] [PMID: 19182785]
[23]
Vincenzi, M.; Mercurio, F.A.; Leone, M. Protein interaction domains and post-translational modifications: structural features and drug discovery applications. Curr. Med. Chem., 2020, 27(37), 6306-6355.
[http://dx.doi.org/10.2174/0929867326666190620101637] [PMID: 31250750]
[24]
Machida, K.; Eschrich, S.; Li, J.; Bai, Y.; Koomen, J.; Mayer, B.J.; Haura, E.B. Characterizing tyrosine phosphorylation signaling in lung cancer using SH2 profiling. PLoS One, 2010, 5(10)e13470
[http://dx.doi.org/10.1371/journal.pone.0013470] [PMID: 20976048]
[25]
Opitz, R.; Müller, M.; Reuter, C.; Barone, M.; Soicke, A.; Roske, Y.; Piotukh, K.; Huy, P.; Beerbaum, M.; Wiesner, B.; Beyermann, M.; Schmieder, P.; Freund, C.; Volkmer, R.; Oschkinat, H.; Schmalz, H.G.; Kühne, R. A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions. Proc. Natl. Acad. Sci. USA, 2015, 112(16), 5011-5016.
[http://dx.doi.org/10.1073/pnas.1422054112] [PMID: 25848013]
[26]
Buday, L.; Downward, J. Epidermal growth factor regulates p21ras through the formation of a complex of receptor, Grb2 adapter protein, and Sos nucleotide exchange factor. Cell, 1993, 73(3), 611-620.
[http://dx.doi.org/10.1016/0092-8674(93)90146-H] [PMID: 8490966]
[27]
Ball, L.J.; Jarchau, T.; Oschkinat, H.; Walter, U. EVH1 domains: structure, function and interactions. FEBS Lett., 2002, 513(1), 45-52.
[http://dx.doi.org/10.1016/S0014-5793(01)03291-4] [PMID: 11911879]
[28]
Sudol, M.; Sliwa, K.; Russo, T. Functions of WW domains in the nucleus. FEBS Lett., 2001, 490(3), 190-195.
[http://dx.doi.org/10.1016/S0014-5793(01)02122-6] [PMID: 11223034]
[29]
Kay, B.K.; Williamson, M.P.; Sudol, M. The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. FASEB J., 2000, 14(2), 231-241.
[http://dx.doi.org/10.1096/fasebj.14.2.231] [PMID: 10657980]
[30]
Kurochkina, N.; Guha, U. SH3 domains: modules of protein-protein interactions. Biophys. Rev., 2013, 5(1), 29-39.
[http://dx.doi.org/10.1007/s12551-012-0081-z] [PMID: 28510178]
[31]
Mayer, B.J. SH3 domains: complexity in moderation. J. Cell Sci., 2001, 114(Pt 7), 1253-1263.
[PMID: 11256992]
[32]
Gmeiner, W.H.; Horita, D.A. Implications of SH3 domain structure and dynamics for protein regulation and drug design. Cell Biochem. Biophys., 2001, 35(2), 127-140.
[http://dx.doi.org/10.1385/CBB:35:2:127] [PMID: 11892788]
[33]
Carducci, M.; Perfetto, L.; Briganti, L.; Paoluzi, S.; Costa, S.; Zerweck, J.; Schutkowski, M.; Castagnoli, L.; Cesareni, G. The protein interaction network mediated by human SH3 domains. Biotechnol. Adv., 2012, 30(1), 4-15.
[http://dx.doi.org/10.1016/j.biotechadv.2011.06.012] [PMID: 21740962]
[34]
Saksela, K.; Permi, P. SH3 domain ligand binding: what’s the consensus and where’s the specificity? FEBS Lett., 2012, 586(17), 2609-2614.
[http://dx.doi.org/10.1016/j.febslet.2012.04.042] [PMID: 22710157]
[35]
Aitio, O.; Hellman, M.; Kesti, T.; Kleino, I.; Samuilova, O.; Pääkkönen, K.; Tossavainen, H.; Saksela, K.; Permi, P. Structural basis of PxxDY motif recognition in SH3 binding. J. Mol. Biol., 2008, 382(1), 167-178.
[http://dx.doi.org/10.1016/j.jmb.2008.07.008] [PMID: 18644376]
[36]
Lim, W.A. Reading between the lines: SH3 recognition of an intact protein. Structure, 1996, 4(6), 657-659.
[http://dx.doi.org/10.1016/S0969-2126(96)00071-8] [PMID: 8805558]
[37]
Teyra, J.; Sidhu, S.S.; Kim, P.M. Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains. FEBS Lett., 2012, 586(17), 2631-2637.
[http://dx.doi.org/10.1016/j.febslet.2012.05.043] [PMID: 22691579]
[38]
Kaneko, T.; Li, L.; Li, S.S. The SH3 domain--a family of versatile peptide- and protein-recognition module. Front. Biosci., 2008, 13, 4938-4952.
[http://dx.doi.org/10.2741/3053] [PMID: 18508559]
[39]
Dikic, I. CIN85/CMS family of adaptor molecules. FEBS Lett., 2002, 529(1), 110-115.
[http://dx.doi.org/10.1016/S0014-5793(02)03188-5] [PMID: 12354621]
[40]
Schnoor, M.; Stradal, T.E.; Rottner, K. Cortactin: cell functions of a multifaceted actin-binding protein. Trends Cell Biol., 2018, 28(2), 79-98.
[http://dx.doi.org/10.1016/j.tcb.2017.10.009] [PMID: 29162307]
[41]
Liu, S.K.; Smith, C.A.; Arnold, R.; Kiefer, F.; McGlade, C.J. The adaptor protein Gads (Grb2-related adaptor downstream of Shc) is implicated in coupling hemopoietic progenitor kinase-1 to the activated TCR. J. Immunol., 2000, 165(3), 1417-1426.
[http://dx.doi.org/10.4049/jimmunol.165.3.1417] [PMID: 10903746]
[42]
Camara-Artigas, A.; Ortiz-Salmeron, E.; Andujar-Sánchez, M.; Bacarizo, J.; Martin-Garcia, J.M. The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase. Acta Crystallogr. F Struct. Biol. Commun., 2016, 72(Pt 9), 707-712.
[http://dx.doi.org/10.1107/S2053230X16012310] [PMID: 27599862]
[43]
Nguyen, J.T.; Porter, M.; Amoui, M.; Miller, W.T.; Zuckermann, R.N.; Lim, W.A. Improving SH3 domain ligand selectivity using a non-natural scaffold. Chem. Biol., 2000, 7(7), 463-473.
[http://dx.doi.org/10.1016/S1074-5521(00)00130-7] [PMID: 10903934]
[44]
Han, S.; Liu, Q.; Wang, F.; Yuan, Z. Targeting the SH3 domain of human osteoclast-stimulating factor with rationally designed peptoid inhibitors. J. Pept. Sci., 2016, 22(8), 533-539.
[http://dx.doi.org/10.1002/psc.2901] [PMID: 27443979]
[45]
Smithgall, T.E. SH2 and SH3 domains: potential targets for anti-cancer drug design. J. Pharmacol. Toxicol. Methods, 1995, 34(3), 125-132.
[http://dx.doi.org/10.1016/1056-8719(95)00082-7] [PMID: 8573762]
[46]
Vohidov, F.; Knudsen, S.E.; Leonard, P.G.; Ohata, J.; Wheadon, M.J.; Popp, B.V.; Ladbury, J.E.; Ball, Z.T. Potent and selective inhibition of SH3 domains with dirhodium metalloinhibitors. Chem. Sci. (Camb.), 2015, 6(8), 4778-4783.
[http://dx.doi.org/10.1039/C5SC01602A] [PMID: 29142714]
[47]
Oneyama, C.; Nakano, H.; Sharma, S.V. UCS15A, a novel small molecule, SH3 domain-mediated protein-protein interaction blocking drug. Oncogene, 2002, 21(13), 2037-2050.
[http://dx.doi.org/10.1038/sj.onc.1205271] [PMID: 11960376]
[48]
Oneyama, C.; Agatsuma, T.; Kanda, Y.; Nakano, H.; Sharma, S.V.; Nakano, S.; Narazaki, F.; Tatsuta, K. Synthetic inhibitors of proline-rich ligand-mediated protein-protein interaction: potent analogs of UCS15A. Chem. Biol., 2003, 10(5), 443-451.
[http://dx.doi.org/10.1016/S1074-5521(03)00101-7] [PMID: 12770826]
[49]
Grover, P.; Shi, H.; Baumgartner, M.; Camacho, C.J.; Smithgall, T.E. Fluorescence polarization screening assays for small molecule allosteric modulators of ABL kinase function. PLoS One, 2015, 10(7)e0133590
[http://dx.doi.org/10.1371/journal.pone.0133590] [PMID: 26222440]
[50]
Chen, S.; Brier, S.; Smithgall, T.E.; Engen, J.R. The Abl SH2-kinase linker naturally adopts a conformation competent for SH3 domain binding. Protein Sci., 2007, 16(4), 572-581.
[http://dx.doi.org/10.1110/ps.062631007] [PMID: 17327393]
[51]
Inglis, S.R.; Stojkoski, C.; Branson, K.M.; Cawthray, J.F.; Fritz, D.; Wiadrowski, E.; Pyke, S.M.; Booker, G.W. Identification and specificity studies of small-molecule ligands for SH3 protein domains. J. Med. Chem., 2004, 47(22), 5405-5417.
[http://dx.doi.org/10.1021/jm049533z] [PMID: 15481978]
[52]
Naisbitt, S.; Kim, E.; Tu, J.C.; Xiao, B.; Sala, C.; Valtschanoff, J.; Weinberg, R.J.; Worley, P.F.; Sheng, M. Shank, a novel family of postsynaptic density proteins that binds to the NMDA receptor/PSD-95/GKAP complex and cortactin. Neuron, 1999, 23(3), 569-582.
[http://dx.doi.org/10.1016/S0896-6273(00)80809-0] [PMID: 10433268]
[53]
Brakeman, P.R.; Lanahan, A.A.; O’Brien, R.; Roche, K.; Barnes, C.A.; Huganir, R.L.; Worley, P.F. Homer: a protein that selectively binds metabotropic glutamate receptors. Nature, 1997, 386(6622), 284-288.
[http://dx.doi.org/10.1038/386284a0] [PMID: 9069287]
[54]
Tu, J.C.; Xiao, B.; Yuan, J.P.; Lanahan, A.A.; Leoffert, K.; Li, M.; Linden, D.J.; Worley, P.F. Homer binds a novel proline-rich motif and links group 1 metabotropic glutamate receptors with IP3 receptors. Neuron, 1998, 21(4), 717-726.
[http://dx.doi.org/10.1016/S0896-6273(00)80589-9] [PMID: 9808459]
[55]
Fedorov, A.A.; Fedorov, E.; Gertler, F.; Almo, S.C. Structure of EVH1, a novel proline-rich ligand-binding module involved in cytoskeletal dynamics and neural function. Nat. Struct. Biol., 1999, 6(7), 661-665.
[http://dx.doi.org/10.1038/10717] [PMID: 10404224]
[56]
Beneken, J.; Tu, J.C.; Xiao, B.; Nuriya, M.; Yuan, J.P.; Worley, P.F.; Leahy, D.J. Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition. Neuron, 2000, 26(1), 143-154.
[http://dx.doi.org/10.1016/S0896-6273(00)81145-9] [PMID: 10798399]
[57]
Peterson, F.C.; Deng, Q.; Zettl, M.; Prehoda, K.E.; Lim, W.A.; Way, M.; Volkman, B.F. Multiple WASP-interacting protein recognition motifs are required for a functional interaction with N-WASP. J. Biol. Chem., 2007, 282(11), 8446-8453.
[http://dx.doi.org/10.1074/jbc.M609902200] [PMID: 17229736]
[58]
Zimmermann, J.; Jarchau, T.; Waltr, U.; Oschkinat, H.; Ball, L.J. Letter to the Editor: H-1, C-13 and N-15 resonance assignment of the human Spred2 EVH1 domain. In: J. Biomol. NMR; , 2004; 29, pp. (3)435-436.
[http://dx.doi.org/10.1023/b:jnmr.0000032526.17586.8c] [PMID: 15213456]
[59]
Le Clainche, C.; Carlier, M.F. Regulation of actin assembly associated with protrusion and adhesion in cell migration. Physiol. Rev., 2008, 88(2), 489-513.
[http://dx.doi.org/10.1152/physrev.00021.2007] [PMID: 18391171]
[60]
Gertler, F.; Condeelis, J. Metastasis: tumor cells becoming MENAcing. Trends Cell Biol., 2011, 21(2), 81-90.
[http://dx.doi.org/10.1016/j.tcb.2010.10.001] [PMID: 21071226]
[61]
Hunke, C.; Hirsch, T.; Eichler, J. Structure-based synthetic mimicry of discontinuous protein binding sites: inhibitors of the interaction of Mena EVH1 domain with proline-rich ligands. ChemBioChem, 2006, 7(8), 1258-1264.
[http://dx.doi.org/10.1002/cbic.200500465] [PMID: 16810654]
[62]
Hopkins, A.L.; Keserü, G.M.; Leeson, P.D.; Rees, D.C.; Reynolds, C.H. The role of ligand efficiency metrics in drug discovery. Nat. Rev. Drug Discov., 2014, 13(2), 105-121.
[http://dx.doi.org/10.1038/nrd4163] [PMID: 24481311]
[63]
Kofler, M.M.; Freund, C. The GYF domain. FEBS J., 2006, 273(2), 245-256.
[http://dx.doi.org/10.1111/j.1742-4658.2005.05078.x] [PMID: 16403013]
[64]
Ash, M.R.; Faelber, K.; Kosslick, D.; Albert, G.I.; Roske, Y.; Kofler, M.; Schuemann, M.; Krause, E.; Freund, C. Conserved beta-hairpin recognition by the GYF domains of Smy2 and GIGYF2 in mRNA surveillance and vesicular transport complexes. Structure, 2010, 18(8), 944-954.
[http://dx.doi.org/10.1016/j.str.2010.04.020] [PMID: 20696395]
[65]
Georgiev, A.; Sjöström, M.; Wieslander, A. Binding specificities of the GYF domains from two Saccharomyces cerevisiae paralogs. Protein Eng. Des. Sel., 2007, 20(9), 443-452.
[http://dx.doi.org/10.1093/protein/gzm041] [PMID: 17804396]
[66]
Freund, C.; Dötsch, V.; Nishizawa, K.; Reinherz, E.L.; Wagner, G. The GYF domain is a novel structural fold that is involved in lymphoid signaling through proline-rich sequences. Nat. Struct. Biol., 1999, 6(7), 656-660.
[http://dx.doi.org/10.1038/10712] [PMID: 10404223]
[67]
Freund, C.; Schmalz, H-G.; Sticht, J.; Kuhne, R. Proteinprotein interactions as new drug targets; Klussmann E., S.J., Ed.; Springer, Berlin; , 2008, 186, pp. 408-422.
[http://dx.doi.org/10.1007/978-3-540-72843-6]
[68]
Ruiz-Martinez, J.; Krebs, C.E.; Makarov, V.; Gorostidi, A.; Martí-Massó, J.F.; Paisán-Ruiz, C. GIGYF2 mutation in late-onset Parkinson’s disease with cognitive impairment. J. Hum. Genet., 2015, 60(10), 637-640.
[http://dx.doi.org/10.1038/jhg.2015.69] [PMID: 26134514 ]
[69]
Kofler, M.; Motzny, K.; Beyermann, M.; Freund, C. Novel interaction partners of the CD2BP2-GYF domain. J. Biol. Chem., 2005, 280(39), 33397-33402.
[http://dx.doi.org/10.1074/jbc.M503989200] [PMID: 16000308]
[70]
Uryga-Polowy, V.; Kosslick, D.; Freund, C.; Rademann, J. Resin-bound aminofluorescein for C-terminal labeling of peptides: high-affinity polarization probes binding to polyproline-specific GYF domains. ChemBioChem, 2008, 9(15), 2452-2462.
[http://dx.doi.org/10.1002/cbic.200800329] [PMID: 18803191]
[71]
Freund, C.; Kühne, R.; Yang, H.; Park, S.; Reinherz, E.L.; Wagner, G. Dynamic interaction of CD2 with the GYF and the SH3 domain of compartmentalized effector molecules. EMBO J., 2002, 21(22), 5985-5995.
[http://dx.doi.org/10.1093/emboj/cdf602] [PMID: 12426371]
[72]
Pornillos, O.; Alam, S.L.; Davis, D.R.; Sundquist, W.I. Structure of the Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein. Nat. Struct. Biol., 2002, 9(11), 812-817.
[http://dx.doi.org/10.1038/nsb856] [PMID: 12379843]
[73]
Pornillos, O.; Alam, S.L.; Rich, R.L.; Myszka, D.G.; Davis, D.R.; Sundquist, W.I. Structure and functional interactions of the Tsg101 UEV domain. EMBO J., 2002, 21(10), 2397-2406.
[http://dx.doi.org/10.1093/emboj/21.10.2397] [PMID: 12006492]
[74]
Yang, X.; Lennard, K.R.; He, C.; Walker, M.C.; Ball, A.T.; Doigneaux, C.; Tavassoli, A.; van der Donk, W.A. A lanthipeptide library used to identify a protein-protein interaction inhibitor. Nat. Chem. Biol., 2018, 14(4), 375-380.
[http://dx.doi.org/10.1038/s41589-018-0008-5] [PMID: 29507389]
[75]
Im, Y.J.; Kuo, L.; Ren, X.; Burgos, P.V.; Zhao, X.Z.; Liu, F.; Burke, T.R. Jr.; Bonifacino, J.S.; Freed, E.O.; Hurley, J.H. Crystallographic and functional analysis of the ESCRT-I /HIV-1 Gag PTAP interaction. Structure, 2010, 18(11), 1536-1547.
[http://dx.doi.org/10.1016/j.str.2010.08.010] [PMID: 21070952]
[76]
Anang, S.; Kaushik, N.; Hingane, S.; Kumari, A.; Gupta, J.; Asthana, S. Shalimar; Nayak, B.; Ranjith-Kumar, C.T.; Surjit, M. Potent inhibition of hepatitis E virus release by a cyclic peptide inhibitor of the interaction between viral open reading frame 3 protein and host tumor susceptibility gene 101. J. Virol., 2018, 92(20), e00684-e00718.
[http://dx.doi.org/10.1128/JVI.00684-18] [PMID: 30068652]
[77]
Srivastava, V.; Verma, P.K. The plant LIM proteins: unlocking the hidden attractions. Planta, 2017, 246(3), 365-375.
[http://dx.doi.org/10.1007/s00425-017-2715-7] [PMID: 28624850]
[78]
Smith, M.A.; Hoffman, L.M.; Beckerle, M.C. LIM proteins in actin cytoskeleton mechanoresponse. Trends Cell Biol., 2014, 24(10), 575-583.
[http://dx.doi.org/10.1016/j.tcb.2014.04.009] [PMID: 24933506]
[79]
Kadrmas, J.L.; Beckerle, M.C. The LIM domain: from the cytoskeleton to the nucleus. Nat. Rev. Mol. Cell Biol., 2004, 5(11), 920-931.
[http://dx.doi.org/10.1038/nrm1499] [PMID: 15520811]
[80]
Dawid, I.B.; Breen, J.J.; Toyama, R. LIM domains: multiple roles as adapters and functional modifiers in protein interactions. Trends Genet., 1998, 14(4), 156-162.
[http://dx.doi.org/10.1016/S0168-9525(98)01424-3] [PMID: 9594664]
[81]
Deane, J.E.; Mackay, J.P.; Kwan, A.H.; Sum, E.Y.; Visvader, J.E.; Matthews, J.M. Structural basis for the recognition of ldb1 by the N-terminal LIM domains of LMO2 and LMO4. EMBO J., 2003, 22(9), 2224-2233.
[http://dx.doi.org/10.1093/emboj/cdg196] [PMID: 12727888]
[82]
Järvinen, P.M.; Laiho, M. LIM-domain proteins in transforming growth factor β-induced epithelial-to-mesenchymal transition and myofibroblast differentiation. Cell. Signal., 2012, 24(4), 819-825.
[http://dx.doi.org/10.1016/j.cellsig.2011.12.004] [PMID: 22182513]
[83]
Sala, S.; Ampe, C. An emerging link between LIM domain proteins and nuclear receptors. Cell. Mol. Life Sci., 2018, 75(11), 1959-1971.
[http://dx.doi.org/10.1007/s00018-018-2774-3] [PMID: 29428964]
[84]
Zheng, Q.; Zhao, Y. The diverse biofunctions of LIM domain proteins: determined by subcellular localization and protein-protein interaction. Biol. Cell, 2007, 99(9), 489-502.
[http://dx.doi.org/10.1042/BC20060126] [PMID: 17696879]
[85]
Li, A.; Ponten, F.; dos Remedios, C.G. The interactome of LIM domain proteins: the contributions of LIM domain proteins to heart failure and heart development. Proteomics, 2012, 12(2), 203-225.
[http://dx.doi.org/10.1002/pmic.201100492] [PMID: 22253135]
[86]
Matthews, J.M.; Lester, K.; Joseph, S.; Curtis, D.J. LIM-domain-only proteins in cancer. Nat. Rev. Cancer, 2013, 13(2), 111-122.
[http://dx.doi.org/10.1038/nrc3418] [PMID: 23303138]
[87]
Tran, M.K.; Kurakula, K.; Koenis, D.S.; de Vries, C.J. Protein-protein interactions of the LIM-only protein FHL2 and functional implication of the interactions relevant in cardiovascular disease. Biochim. Biophys. Acta, 2016, 1863(2), 219-228.
[http://dx.doi.org/10.1016/j.bbamcr.2015.11.002] [PMID: 26548523]
[88]
Liang, Y.; Bradford, W.H.; Zhang, J.; Sheikh, F. Four and a half LIM domain protein signaling and cardiomyopathy. Biophys. Rev., 2018, 10(4), 1073-1085.
[http://dx.doi.org/10.1007/s12551-018-0434-3] [PMID: 29926425]
[89]
Grunewald, T.G.; Butt, E. The LIM and SH3 domain protein family: structural proteins or signal transducers or both? Mol. Cancer, 2008, 7, 31.
[http://dx.doi.org/10.1186/1476-4598-7-31] [PMID: 18419822]
[90]
Prunier, C.; Prudent, R.; Kapur, R.; Sadoul, K.; Lafanechère, L. LIM kinases: cofilin and beyond. Oncotarget, 2017, 8(25), 41749-41763.
[http://dx.doi.org/10.18632/oncotarget.16978] [PMID: 28445157]
[91]
Nam, C.H.; Lobato, M.N.; Appert, A.; Drynan, L.F.; Tanaka, T.; Rabbitts, T.H. An antibody inhibitor of the LMO2-protein complex blocks its normal and tumorigenic functions. Oncogene, 2008, 27(36), 4962-4968.
[http://dx.doi.org/10.1038/onc.2008.130] [PMID: 18438427]
[92]
Appert, A.; Nam, C.H.; Lobato, N.; Priego, E.; Miguel, R.N.; Blundell, T.; Drynan, L.; Sewell, H.; Tanaka, T.; Rabbitts, T. Targeting LMO2 with a peptide aptamer establishes a necessary function in overt T-cell neoplasia. Cancer Res., 2009, 69(11), 4784-4790.
[http://dx.doi.org/10.1158/0008-5472.CAN-08-4774] [PMID: 19487290]
[93]
Harrison, B.A.; Almstead, Z.Y.; Burgoon, H.; Gardyan, M.; Goodwin, N.C.; Healy, J.; Liu, Y.; Mabon, R.; Marinelli, B.; Samala, L.; Zhang, Y.; Stouch, T.R.; Whitlock, N.A.; Gopinathan, S.; McKnight, B.; Wang, S.; Patel, N.; Wilson, A.G.E.; Hamman, B.D.; Rice, D.S.; Rawlins, D.B. Discovery and development of LX7101, a dual LIM-kinase and ROCK inhibitor for the treatment of glaucoma. ACS Med. Chem. Lett., 2014, 6(1), 84-88.
[http://dx.doi.org/10.1021/ml500367g] [PMID: 25589936]
[94]
Stradal, T.; Kranewitter, W.; Winder, S.J.; Gimona, M. CH domains revisited. FEBS Lett., 1998, 431(2), 134-137.
[http://dx.doi.org/10.1016/S0014-5793(98)00751-0] [PMID: 9708889]
[95]
Bramham, J.; Hodgkinson, J.L.; Smith, B.O.; Uhrín, D.; Barlow, P.N.; Winder, S.J. Solution structure of the calponin CH domain and fitting to the 3D-helical reconstruction of F-actin:calponin. Structure, 2002, 10(2), 249-258.
[http://dx.doi.org/10.1016/S0969-2126(02)00703-7] [PMID: 11839310]
[96]
Lorenz, S.; Vakonakis, I.; Lowe, E.D.; Campbell, I.D.; Noble, M.E.M.; Hoellerer, M.K. Structural analysis of the interactions between paxillin LD motifs and alpha-parvin. Structure, 2008, 16(10), 1521-1531.
[http://dx.doi.org/10.1016/j.str.2008.08.007] [PMID: 18940607]
[97]
Sjöblom, B.; Ylänne, J.; Djinović-Carugo, K. Novel structural insights into F-actin-binding and novel functions of calponin homology domains. Curr. Opin. Struct. Biol., 2008, 18(6), 702-708.
[http://dx.doi.org/10.1016/j.sbi.2008.10.003] [PMID: 18952167]
[98]
Galkin, V.E.; Orlova, A.; Cherepanova, O.; Lebart, M.C.; Egelman, E.H. High-resolution cryo-EM structure of the F-actin-fimbrin/plastin ABD2 complex. Proc. Natl. Acad. Sci. USA, 2008, 105(5), 1494-1498.
[http://dx.doi.org/10.1073/pnas.0708667105] [PMID: 18234857]
[99]
Klein, M.G.; Shi, W.; Ramagopal, U.; Tseng, Y.; Wirtz, D.; Kovar, D.R.; Staiger, C.J.; Almo, S.C. Structure of the actin crosslinking core of fimbrin. Structure, 2004, 12(6), 999-1013.
[http://dx.doi.org/10.1016/j.str.2004.04.010] [PMID: 15274920]
[100]
Gimona, M.; Winder, S.J. The calponin homology (CH) domain; Protein Science Encyclopedia, 2008.
[http://dx.doi.org/10.1002/9783527610754.pp02]
[101]
Beggs, A.H.; Hoffman, E.P.; Snyder, J.R.; Arahata, K.; Specht, L.; Shapiro, F.; Angelini, C.; Sugita, H.; Kunkel, L.M. Exploring the molecular basis for variability among patients with Becker muscular dystrophy: dystrophin gene and protein studies. Am. J. Hum. Genet., 1991, 49(1), 54-67.
[PMID: 2063877]
[102]
Roberts, R.G.; Gardner, R.J.; Bobrow, M. Searching for the 1 in 2,400,000: a review of dystrophin gene point mutations. Hum. Mutat., 1994, 4(1), 1-11.
[http://dx.doi.org/10.1002/humu.1380040102] [PMID: 7951253]
[103]
Robertson, S.P.; Twigg, S.R.; Sutherland-Smith, A.J.; Biancalana, V.; Gorlin, R.J.; Horn, D.; Kenwrick, S.J.; Kim, C.A.; Morava, E.; Newbury-Ecob, R.; Orstavik, K.H.; Quarrell, O.W.; Schwartz, C.E.; Shears, D.J.; Suri, M.; Kendrick-Jones, J.; Wilkie, A.O. OPD-spectrum disorders clinical collaborative group. Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans. Nat. Genet., 2003, 33(4), 487-491.
[http://dx.doi.org/10.1038/ng1119] [PMID: 12612583]
[104]
Hassoun, H.; Vassiliadis, J.N.; Murray, J.; Njolstad, P.R.; Rogus, J.J.; Ballas, S.K.; Schaffer, F.; Jarolim, P.; Brabec, V.; Palek, J. Characterization of the underlying molecular defect in hereditary spherocytosis associated with spectrin deficiency. Blood, 1997, 90(1), 398-406.
[PMID: 9207476]
[105]
Kim, S.; Cullis, D.N.; Feig, L.A.; Baleja, J.D. Solution structure of the Reps1 EH domain and characterization of its binding to NPF target sequences. Biochemistry, 2001, 40(23), 6776-6785.
[http://dx.doi.org/10.1021/bi002700m] [PMID: 11389591]
[106]
Naslavsky, N.; Caplan, S. EHD proteins: key conductors of endocytic transport. Trends Cell Biol., 2011, 21(2), 122-131.
[http://dx.doi.org/10.1016/j.tcb.2010.10.003] [PMID: 21067929]
[107]
Ioannou, M.S.; Marat, A.L. The role of EHD proteins at the neuronal synapse. Sci. Signal., 2012, 5(221), jc1.
[http://dx.doi.org/10.1126/scisignal.2002989] [PMID: 22534130]
[108]
Miliaras, N.B.; Wendland, B. EH proteins: multivalent regulators of endocytosis (and other pathways). Cell Biochem. Biophys., 2004, 41(2), 295-318.
[http://dx.doi.org/10.1385/CBB:41:2:295] [PMID: 15475615]
[109]
de Beer, T.; Hoofnagle, A.N.; Enmon, J.L.; Bowers, R.C.; Yamabhai, M.; Kay, B.K.; Overduin, M. Molecular mechanism of NPF recognition by EH domains. Nat. Struct. Biol., 2000, 7(11), 1018-1022.
[http://dx.doi.org/10.1038/80924] [PMID: 11062555]
[110]
de Beer, T.; Carter, R.E.; Lobel-Rice, K.E.; Sorkin, A.; Overduin, M. Structure and Asn-Pro-Phe binding pocket of the Eps15 homology domain. Science, 1998, 281(5381), 1357-1360.
[http://dx.doi.org/10.1126/science.281.5381.1357] [PMID: 9721102]
[111]
Kamens, A.J.; Mientkiewicz, K.M.; Eisert, R.J.; Walz, J.A.; Mace, C.R.; Kritzer, J.A. Thioether-stapled macrocyclic inhibitors of the EH domain of EHD1. Bioorg. Med. Chem., 2018, 26(6), 1206-1211.
[http://dx.doi.org/10.1016/j.bmc.2017.09.007] [PMID: 28951093]
[112]
Kamens, A.J.; Eisert, R.J.; Corlin, T.; Baleja, J.D.; Kritzer, J.A. Structured cyclic peptides that bind the EH domain of EHD1. Biochemistry, 2014, 53(29), 4758-4760.
[http://dx.doi.org/10.1021/bi500744q] [PMID: 25014215]
[113]
Khan, Z.; Lafon, M. PDZ domain-mediated protein interactions: therapeutic targets in neurological disorders. Curr. Med. Chem., 2014, 21(23), 2632-2641.
[http://dx.doi.org/10.2174/0929867321666140303145312] [PMID: 24606518]
[114]
Fanning, A.S.; Anderson, J.M. Protein-protein interactions: PDZ domain networks. Curr. Biol., 1996, 6(11), 1385-1388.
[http://dx.doi.org/10.1016/S0960-9822(96)00737-3] [PMID: 8939589]
[115]
Ranganathan, R.; Ross, E.M. PDZ domain proteins: scaffolds for signaling complexes. Curr. Biol., 1997, 7(12), R770-R773.
[http://dx.doi.org/10.1016/S0960-9822(06)00401-5] [PMID: 9382826]
[116]
Hata, Y.; Nakanishi, H.; Takai, Y. Synaptic PDZ domain-containing proteins. Neurosci. Res., 1998, 32(1), 1-7.
[http://dx.doi.org/10.1016/S0168-0102(98)00069-8] [PMID: 9831248]
[117]
Fan, J.S.; Zhang, M. Signaling complex organization by PDZ domain proteins. Neurosignals, 2002, 11(6), 315-321.
[http://dx.doi.org/10.1159/000068256] [PMID: 12566920]
[118]
Jeleń, F.; Oleksy, A.; Smietana, K.; Otlewski, J. PDZ domains - common players in the cell signaling. Acta Biochim. Pol., 2003, 50(4), 985-1017.
[http://dx.doi.org/10.18388/abp.2003_3628] [PMID: 14739991]
[119]
Lee, H-J.; Zheng, J.J. PDZ domains and their binding partners: structure, specificity, and modification. Cell Commun. Signal., 2010, 8, 8.
[http://dx.doi.org/10.1186/1478-811X-8-8] [PMID: 20509869]
[120]
Saras, J.; Heldin, C.H. PDZ domains bind carboxy-terminal sequences of target proteins. Trends Biochem. Sci., 1996, 21(12), 455-458.
[http://dx.doi.org/10.1016/S0968-0004(96)30044-3] [PMID: 9009824]
[121]
Kim, E.; Sheng, M. PDZ domain proteins of synapses. Nat. Rev. Neurosci., 2004, 5(10), 771-781.
[http://dx.doi.org/10.1038/nrn1517] [PMID: 15378037]
[122]
Garner, C.C.; Nash, J.; Huganir, R.L. PDZ domains in synapse assembly and signalling. Trends Cell Biol., 2000, 10(7), 274-280.
[http://dx.doi.org/10.1016/S0962-8924(00)01783-9] [PMID: 10856930]
[123]
Ponting, C.P.; Phillips, C.; Davies, K.E.; Blake, D.J. PDZ domains: targeting signalling molecules to sub-membranous sites. BioEssays, 1997, 19(6), 469-479.
[http://dx.doi.org/10.1002/bies.950190606] [PMID: 9204764]
[124]
Ivarsson, Y. Plasticity of PDZ domains in ligand recognition and signaling. FEBS Lett., 2012, 586(17), 2638-2647.
[http://dx.doi.org/10.1016/j.febslet.2012.04.015] [PMID: 22576124]
[125]
Harris, B.Z.; Lim, W.A. Mechanism and role of PDZ domains in signaling complex assembly. J. Cell Sci., 2001, 114(Pt 18), 3219-3231.
[http://dx.doi.org/10.1126/stke.2003.179.re7] [PMID: 11591811]
[126]
Nourry, C.; Grant, S.G.; Borg, J-P. PDZ domain proteins: plug and play! Sci. STKE, 2003, 2003(179), RE7.
[http://dx.doi.org/10.1126/stke.2003.179.re7] [PMID: 12709532]
[127]
Zhang, M.; Wang, W. Organization of signaling complexes by PDZ-domain scaffold proteins. Acc. Chem. Res., 2003, 36(7), 530-538.
[http://dx.doi.org/10.1021/ar020210b] [PMID: 12859214]
[128]
Ivanov, A.S.; Gnedenko, O.V.; Molnar, A.A.; Mezentsev, Y.V.; Lisitsa, A.V.; Archakov, A.I. Protein-protein interactions as new targets for drug design: virtual and experimental approaches. J. Bioinform. Comput. Biol., 2007, 5(2B), 579-592.
[http://dx.doi.org/10.1142/S0219720007002825] [PMID: 17636863]
[129]
Fanning, A.S.; Lye, M.F.; Anderson, J.M.; Lavie, A. Domain swapping within PDZ2 is responsible for dimerization of ZO proteins. J. Biol. Chem., 2007, 282(52), 37710-37716.
[http://dx.doi.org/10.1074/jbc.M707255200] [PMID: 17928286]
[130]
Grillo-Bosch, D.; Choquet, D.; Sainlos, M. Inhibition of PDZ domain-mediated interactions. Drug Discov. Today. Technol., 2013, 10(4), e531-e540.
[http://dx.doi.org/10.1016/j.ddtec.2012.10.003] [PMID: 24451645]
[131]
Hori, K.; Ajioka, K.; Goda, N.; Shindo, A.; Takagishi, M.; Tenno, T.; Hiroaki, H. Discovery of potent disheveled/Dvl inhibitors using virtual screening optimized with NMR-based docking performance index. Front. Pharmacol., 2018, 9, 983.
[http://dx.doi.org/10.3389/fphar.2018.00983] [PMID: 30233369]
[132]
Shan, J.; Zhang, X.; Bao, J.; Cassell, R.; Zheng, J.J. Synthesis of potent dishevelled PDZ domain inhibitors guided by virtual screening and NMR studies. Chem. Biol. Drug Des., 2012, 79(4), 376-383.
[http://dx.doi.org/10.1111/j.1747-0285.2011.01295.x] [PMID: 22172211]
[133]
Thorsen, T.S.; Madsen, K.L.; Rebola, N.; Rathje, M.; Anggono, V.; Bach, A.; Moreira, I.S.; Stuhr-Hansen, N.; Dyhring, T.; Peters, D.; Beuming, T.; Huganir, R.; Weinstein, H.; Mulle, C.; Strømgaard, K.; Rønn, L.C.B.; Gether, U. Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD. Proc. Natl. Acad. Sci. USA, 2010, 107(1), 413-418.
[http://dx.doi.org/10.1073/pnas.0902225107] [PMID: 20018661]
[134]
Saupe, J.; Roske, Y.; Schillinger, C.; Kamdem, N.; Radetzki, S.; Diehl, A.; Oschkinat, H.; Krause, G.; Heinemann, U.; Rademann, J. Discovery, structure-activity relationship studies, and crystal structure of nonpeptide inhibitors bound to the Shank3 PDZ domain. ChemMedChem, 2011, 6(8), 1411-1422.
[http://dx.doi.org/10.1002/cmdc.201100094] [PMID: 21626699]
[135]
Bach, A.; Clausen, B.H.; Møller, M.; Vestergaard, B.; Chi, C.N.; Round, A.; Sørensen, P.L.; Nissen, K.B.; Kastrup, J.S.; Gajhede, M.; Jemth, P.; Kristensen, A.S.; Lundström, P.; Lambertsen, K.L.; Strømgaard, K. A high-affinity, dimeric inhibitor of PSD-95 bivalently interacts with PDZ1-2 and protects against ischemic brain damage. Proc. Natl. Acad. Sci. USA, 2012, 109(9), 3317-3322.
[http://dx.doi.org/10.1073/pnas.1113761109] [PMID: 22343531]
[136]
Bach, A.; Chi, C.N.; Pang, G.F.; Olsen, L.; Kristensen, A.S.; Jemth, P.; Strømgaard, K. Design and synthesis of highly potent and plasma-stable dimeric inhibitors of the PSD-95-NMDA receptor interaction. Angew. Chem. Int. Ed. Engl., 2009, 48(51), 9685-9689.
[http://dx.doi.org/10.1002/anie.200904741] [PMID: 19937879]
[137]
Caillet-Saguy, C.; Maisonneuve, P.; Delhommel, F.; Terrien, E.; Babault, N.; Lafon, M.; Cordier, F.; Wolff, N. Strategies to interfere with PDZ-mediated interactions in neurons: What we can learn from the rabies virus. Prog. Biophys. Mol. Biol., 2015, 119(1), 53-59.
[http://dx.doi.org/10.1016/j.pbiomolbio.2015.02.007] [PMID: 25748547]
[138]
Babault, N.; Cordier, F.; Lafage, M.; Cockburn, J.; Haouz, A.; Prehaud, C.; Rey, F.A.; Delepierre, M.; Buc, H.; Lafon, M.; Wolff, N. Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death. Structure, 2011, 19(10), 1518-1524.
[http://dx.doi.org/10.1016/j.str.2011.07.007] [PMID: 22000519]
[139]
Hammond, M.C.; Harris, B.Z.; Lim, W.A.; Bartlett, P.A. Beta strand peptidomimetics as potent PDZ domain ligands. Chem. Biol., 2006, 13(12), 1247-1251.
[http://dx.doi.org/10.1016/j.chembiol.2006.11.010] [PMID: 17185220]
[140]
Piserchio, A.; Salinas, G.D.; Li, T.; Marshall, J.; Spaller, M.R.; Mierke, D.F. Targeting specific PDZ domains of PSD-95; structural basis for enhanced affinity and enzymatic stability of a cyclic peptide. Chem. Biol., 2004, 11(4), 469-473.
[http://dx.doi.org/10.1016/j.chembiol.2004.03.013] [PMID: 15123241]
[141]
Patra, C.R.; Rupasinghe, C.N.; Dutta, S.K.; Bhattacharya, S.; Wang, E.; Spaller, M.R.; Mukhopadhyay, D. Chemically modified peptides targeting the PDZ domain of GIPC as a therapeutic approach for cancer. ACS Chem. Biol., 2012, 7(4), 770-779.
[http://dx.doi.org/10.1021/cb200536r] [PMID: 22292614]
[142]
Vincenzi, M.; Mercurio, F.A.; Leone, M. Sam domains in multiple diseases. Curr. Med. Chem., 2020, 27(3), 450-476.
[http://dx.doi.org/10.2174/0929867325666181009114445] [PMID: 30306850]
[143]
Kim, C.A.; Bowie, J.U. SAM domains: uniform structure, diversity of function. Trends Biochem. Sci., 2003, 28(12), 625-628.
[http://dx.doi.org/10.1016/j.tibs.2003.11.001] [PMID: 14659692]
[144]
Knight, M.J.; Leettola, C.; Gingery, M.; Li, H.; Bowie, J.U. A human sterile alpha motif domain polymerizome. Protein Sci., 2011, 20(10), 1697-1706.
[http://dx.doi.org/10.1002/pro.703] [PMID: 21805519]
[145]
Neira, J.L.; Díaz-García, C.; Prieto, M.; Coutinho, A. The C-terminal SAM domain of p73 binds to the N terminus of MDM2. Biochim. Biophys. Acta, Gen. Subj., 2019, 1863(4), 760-770.
[http://dx.doi.org/10.1016/j.bbagen.2019.01.019] [PMID: 30735716]
[146]
Mercurio, F.A.; Leone, M. The sam domain of EphA2 receptor and its relevance to cancer: a novel challenge for drug discovery? Curr. Med. Chem., 2016, 23(42), 4718-4734.
[http://dx.doi.org/10.2174/0929867323666161101100722] [PMID: 27804871]
[147]
Kukuk, L.; Dingley, A.J.; Granzin, J.; Nagel-Steger, L.; Thiagarajan-Rosenkranz, P.; Ciupka, D.; Hänel, K.; Batra-Safferling, R.; Pacheco, V.; Stoldt, M.; Pfeffer, K.; Beer-Hammer, S.; Willbold, D.; Koenig, B.W. Structure of the SLy1 SAM homodimer reveals a new interface for SAM domain self-association. Sci. Rep., 2019, 9(1), 54.
[http://dx.doi.org/10.1038/s41598-018-37185-3] [PMID: 30631134]
[148]
Kong, J.; Wang, M.M.; He, S.Y.; Peng, X.; Qin, X.H. Structural characterization and directed modification of Sus scrofa SAMHD1 reveal the mechanism underlying deoxynucleotide regulation. FEBS J., 2019, 286(19), 3844-3857.
[http://dx.doi.org/10.1111/febs.14943] [PMID: 31152619]
[149]
Leone, M.; Cellitti, J.; Pellecchia, M. NMR studies of a heterotypic Sam-Sam domain association: the interaction between the lipid phosphatase Ship2 and the EphA2 receptor. Biochemistry, 2008, 47(48), 12721-12728.
[http://dx.doi.org/10.1021/bi801713f] [PMID: 18991394]
[150]
Mercurio, F.A.; Marasco, D.; Pirone, L.; Pedone, E.M.; Pellecchia, M.; Leone, M. Solution structure of the first Sam domain of Odin and binding studies with the EphA2 receptor. Biochemistry, 2012, 51(10), 2136-2145.
[http://dx.doi.org/10.1021/bi300141h] [PMID: 22332920]
[151]
Mercurio, F.A.; Marasco, D.; Pirone, L.; Scognamiglio, P.L.; Pedone, E.M.; Pellecchia, M.; Leone, M. Heterotypic Sam-Sam association between Odin-Sam1 and Arap3-Sam: binding affinity and structural insights. ChemBioChem, 2013, 14(1), 100-106.
[http://dx.doi.org/10.1002/cbic.201200592] [PMID: 23239578]
[152]
Wang, Y.; Shang, Y.; Li, J.; Chen, W.; Li, G.; Wan, J.; Liu, W.; Zhang, M. Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions. eLife, 2018, 7e35677
[http://dx.doi.org/10.7554/eLife.35677] [PMID: 29749928]
[153]
Kim, C.A.; Sawaya, M.R.; Cascio, D.; Kim, W.; Bowie, J.U. Structural organization of a sex-comb-on-midleg/polyhomeotic copolymer. J. Biol. Chem., 2005, 280(30), 27769-27775.
[http://dx.doi.org/10.1074/jbc.M503055200] [PMID: 15905166]
[154]
Rajakulendran, T.; Sahmi, M.; Kurinov, I.; Tyers, M.; Therrien, M.; Sicheri, F. CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling. Proc. Natl. Acad. Sci. USA, 2008, 105(8), 2836-2841.
[http://dx.doi.org/10.1073/pnas.0709705105] [PMID: 18287031]
[155]
Stafford, R.L.; Hinde, E.; Knight, M.J.; Pennella, M.A.; Ear, J.; Digman, M.A.; Gratton, E.; Bowie, J.U. Tandem SAM domain structure of human Caskin1: a presynaptic, self-assembling scaffold for CASK. Structure, 2011, 19(12), 1826-1836.
[http://dx.doi.org/10.1016/j.str.2011.09.018] [PMID: 22153505]
[156]
Leettola, C.N.; Knight, M.J.; Cascio, D.; Hoffman, S.; Bowie, J.U. Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3. BMC Struct. Biol., 2014, 14, 17.
[http://dx.doi.org/10.1186/1472-6807-14-17] [PMID: 24998259]
[157]
Thanos, C.D.; Goodwill, K.E.; Bowie, J.U. Oligomeric structure of the human EphB2 receptor SAM domain. Science, 1999, 283(5403), 833-836.
[http://dx.doi.org/10.1126/science.283.5403.833] [PMID: 9933164]
[158]
Zhuang, G.; Hunter, S.; Hwang, Y.; Chen, J. Regulation of EphA2 receptor endocytosis by SHIP2 lipid phosphatase via phosphatidylinositol 3-Kinase-dependent Rac1 activation. J. Biol. Chem., 2007, 282(4), 2683-2694.
[http://dx.doi.org/10.1074/jbc.M608509200] [PMID: 17135240]
[159]
Kim, J.; Lee, H.; Kim, Y.; Yoo, S.; Park, E.; Park, S. The SAM domains of Anks family proteins are critically involved in modulating the degradation of EphA receptors. Mol. Cell. Biol., 2010, 30(7), 1582-1592.
[http://dx.doi.org/10.1128/MCB.01605-09] [PMID: 20100865]
[160]
Lee, H.J.; Hota, P.K.; Chugha, P.; Guo, H.; Miao, H.; Zhang, L.; Kim, S.J.; Stetzik, L.; Wang, B.C.; Buck, M. NMR structure of a heterodimeric SAM:SAM complex: characterization and manipulation of EphA2 binding reveal new cellular functions of SHIP2. Structure, 2012, 20(1), 41-55.
[http://dx.doi.org/10.1016/j.str.2011.11.013] [PMID: 22244754]
[161]
Mercurio, F.A.; Scognamiglio, P.L.; Di Natale, C.; Marasco, D.; Pellecchia, M.; Leone, M. CD and NMR conformational studies of a peptide encompassing the Mid Loop interface of Ship2-Sam. Biopolymers, 2014, 101(11), 1088-1098.
[http://dx.doi.org/10.1002/bip.22512] [PMID: 24889333]
[162]
Mercurio, F.A.; Di Natale, C.; Pirone, L.; Scognamiglio, P.L.; Marasco, D.; Pedone, E.M.; Saviano, M.; Leone, M. Peptide fragments of odin-sam1: conformational analysis and interaction studies with EphA2-sam. ChemBioChem, 2015, 16(11), 1629-1636.
[http://dx.doi.org/10.1002/cbic.201500197] [PMID: 26120079]
[163]
Mercurio, F.A.; Marasco, D.; Di Natale, C.; Pirone, L.; Costantini, S.; Pedone, E.M.; Leone, M. Targeting EphA2-Sam and its interactome: design and evaluation of helical peptides enriched in charged residues. ChemBioChem, 2016, 17(22), 2179-2188.
[http://dx.doi.org/10.1002/cbic.201600413] [PMID: 27763725]
[164]
Mercurio, F.A.; Di Natale, C.; Pirone, L.; Iannitti, R.; Marasco, D.; Pedone, E.M.; Palumbo, R.; Leone, M. The Sam-Sam interaction between Ship2 and the EphA2 receptor: design and analysis of peptide inhibitors. Sci. Rep., 2017, 7(1), 17474.
[http://dx.doi.org/10.1038/s41598-017-17684-5] [PMID: 29234063]
[165]
Mercurio, F.A.; Pirone, L.; Di Natale, C.; Marasco, D.; Pedone, E.M.; Leone, M. Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2. Bioorg. Chem., 2018, 80, 602-610.
[http://dx.doi.org/10.1016/j.bioorg.2018.07.013] [PMID: 30036816]
[166]
Mercurio, F.A.; Di Natale, C.; Pirone, L.; Marasco, D.; Calce, E.; Vincenzi, M.; Pedone, E.M.; De Luca, S.; Leone, M. Design and analysis of EphA2-SAM peptide ligands: a multi-disciplinary screening approach. Bioorg. Chem., 2019, 84, 434-443.
[http://dx.doi.org/10.1016/j.bioorg.2018.12.009] [PMID: 30576907]
[167]
Fraley, T.S.; Tran, T.C.; Corgan, A.M.; Nash, C.A.; Hao, J.; Critchley, D.R.; Greenwood, J.A. Phosphoinositide binding inhibits alpha-actinin bundling activity. J. Biol. Chem., 2003, 278(26), 24039-24045.
[http://dx.doi.org/10.1074/jbc.M213288200] [PMID: 12716899]

Rights & Permissions Print Cite
Article Metrics
76
1
Wayfinder Image
© 2024 Bentham Science Publishers | Privacy Policy